Insight into the symbiotic lifestyle of DPANN archaea revealed by cultivation and genome analyses

Significance

The DPANN superphylum is a grouping of symbiotic microorganisms categorized based on their genomic contents and a few examples of cultivation experiments. Although the genome information of DPANN archaea is increasing year by year, most of them have remained uncultivated, limiting our knowledge of these organisms. Herein, a thermoacidophilic symbiotic archaeon (ARM-1) from the DPANN superphylum was successfully cultivated and characterized. We determined its physiological, morphological, and genomic characteristics in detail and obtained experimental evidence of the symbiotic lifestyle of this archaeon. Notably, ARM-1 is a symbiotic archaeal strain that showed dependence on a range of host species in a laboratory culture. The results significantly contribute to the true understanding of the physiology and ecology of DPANN archaea.

Abstract

Decades of culture-independent analyses have resulted in proposals of many tentative archaeal phyla with no cultivable representative. Members of DPANN (an acronym of the names of the first included phyla Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanohaloarchaeota, and Nanoarchaeota), an archaeal superphylum composed of at least 10 of these tentative phyla, are generally considered obligate symbionts dependent on other microorganisms. While many draft/complete genome sequences of DPANN archaea are available and their biological functions have been considerably predicted, only a few examples of their successful laboratory cultivation have been reported, limiting our knowledge of their symbiotic lifestyles. Here, we investigated physiology, morphology, and host specificity of an archaeon of the phylum “Candidatus Micrarchaeota” (ARM-1) belonging to the DPANN superphylum by cultivation. We constructed a stable coculture system composed of ARM-1 and its original host Metallosphaera sp. AS-7 belonging to the order Sulfolobales. Further host-switching experiments confirmed that ARM-1 grew on five different archaeal species from three genera—Metallosphaera, Acidianus, and Saccharolobus—originating from geologically distinct hot, acidic environments. The results suggested the existence of DPANN archaea that can grow by relying on a range of hosts. Genomic analyses showed inferred metabolic capabilities, common/unique genetic contents of ARM-1 among cultivated micrarchaeal representatives, and the possibility of horizontal gene transfer between ARM-1 and members of the order Sulfolobales. Our report sheds light on the symbiotic lifestyles of DPANN archaea and will contribute to the elucidation of their biological/ecological functions.

Footnotes

    • Accepted November 12, 2021.
  • Author contributions: H.D.S., A.S., and N.K. designed research; H.D.S., N.N., A.S., and N.K. performed research; N.N. and N.K. performed field sampling; H.D.S., M.Y., and M.S. contributed new reagents/analytic tools; H.D.S., S.K., T.I., and M.O. analyzed data; and H.D.S. and N.K. wrote the paper.

  • The authors declare no competing interest.

  • This article is a PNAS Direct Submission.

  • This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.2115449119/-/DCSupplemental.

Data Availability

Sequence data of 16S rRNA genes supporting the findings of this study have been deposited in GenBank under accession nos. LC490573LC490578. Genomic sequences of ARM-1 and Metallosphaera sp. AS-7 with raw read data have been deposited under the following accession nos.: AP024486 (ARM-1 genome), AP024487 (AS-7 genome), DRR248897 (PacBio RS II long reads), and DRR248898 (Illumina MiSeq short reads). All study data are included in the article and/or supporting information.

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